1. Summary Candida species are a frequent and serious cause of bloodstream infections in the clinic. Despite access to several antifungal drugs, systemic infections are associated with mortality rates that can exceed 40%. In many patients, the organism persists in the bloodstream during antifungal treatment, despite the fact that recovered isolates are not drug resistant when tested in vitro. The mechanisms responsible for such clinical persistence are unknown, but persistence is critically associated with therapeutic failure, recurrent infection and reduced survival. Our preliminary studies indicate that persistence of Candida albicans infections is associated with the ability of isolates to exhibit cryptic growth at drug concentrations above inhibitory levels, a phenomenon now termed perseverance. We show that perseverance reflects the proportion of the population that can grow at supra-MIC drug concentrations, is concentration-independent, and does not correlate with drug resistance levels. Moreover, isolates that persist in the clinic also harbor subpopulations of cells which display transient but elevated levels of resistance, a phenomenon previously described as heteroresistance. Here, we propose to use genetic and genomic approaches to define the mechanisms underlying perseverance and heteroresistance in C. albicans. We will first perform a genetic screen and in vitro profiling to determine how these isolates respond to antifungal challenge, and to identify the properties that enable persistent isolates to resist antifungal therapy. To complement this approach, genomics and transcriptional profiling will directly compare sets of C. albicans isolates from persistent and nonpersistent infections. Finally, genomics will also be used to define how heteroresistant cells differ from the majority of cells in the original population. Together, these studies will identify those properties that enable a subset of C. albicans strains to evade drug treatment and prolong systemic infection. These insights can then be used to establish more effective treatment regimens against this pervasive human fungal pathogen.